Youve got the ANTHOXANTHIN Blues. This chemical, along with a bunch of other unique ones in the onion family, will react with Aluminum or carbon steel in acidic media to turn brown. SO where you have cross cuts on the onion you would have these chemicals forming the deep brown precipitates.
I know, from Cooks Country, they stated that you oughta do all the normal cooking fiorst and then gradually bring up the acid >AND dont cook in ALuminum clad pans when you do this type pof processing. Potatoes have these anthoxanthisn too and thats why they turn black at the "eye nodes" .
I dont think it hurts anything as far as palatability or safety, maybe whenever you pull some shallots from the jar, just grab the end with tongs and slip the ends off. Youll still have a small spot but it wont be too objectionable.
This happens a lot anyway, we just keep the A,uminum clad pots (everybpdy has some) on a back side of the pot rack.